I did and got the following to test freesurfer installation according to freesurfer website directions: [marcos@alien ~]$ tkmedit bert orig.mgz
=================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : ___________________________________ the contents of .xdebug_tkmedit: tkmedit started: Sat Mar 9 14:16:07 2013
/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz
$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/marcos Set subject home dir to /usr/local/freesurfer/subjects/bert
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27f84ab0, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00:
___________________________________ running bugr I got: FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
RedHat release: Fedora release 18 (Spherical Cow)
Kernel info: Linux 3.8.1-201.fc18.x86_64 x86_64
___________________________________ Additional environment info: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
___________________________________ [marcos@alien ~]$ which tkmedit /usr/local/freesurfer/bin/tkmedit ___________________________________
I did the installation according website. My only additional step was to install tcsh because when I tried tkmedit it returned: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: File or directory not found.
My machine is an Alienware MX17R2 with 8GB RAM and Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz (Quadcore) My video from lspci is Advanced Micro Devices [AMD] nee ATI Broadway XT [Mobility Radeon HD 5800 Series] and I am using native drivers instead of AMD proprietary driver
thank you for your support
Marcos,
Does mri_convert work? What version of tcsh was installed? Maybe you can try the freesurfer centos4_x86_64 distribution? We havent tested on Fedora 18 so we havent seen this before.
Nick
On Sat, 2013-03-09 at 16:11 -0300, Marcos Martins da Silva wrote:
I did and got the following to test freesurfer installation according to freesurfer website directions: [marcos@alien ~]$ tkmedit bert orig.mgz
=================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : ___________________________________ the contents of .xdebug_tkmedit: tkmedit started: Sat Mar 9 14:16:07 2013
/usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/marcos Set subject home dir to /usr/local/freesurfer/subjects/bert
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27f84ab0, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00:
running bugr I got: FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
RedHat release: Fedora release 18 (Spherical Cow)
Kernel info: Linux 3.8.1-201.fc18.x86_64 x86_64
Additional environment info: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
[marcos@alien ~]$ which tkmedit /usr/local/freesurfer/bin/tkmedit ___________________________________
I did the installation according website. My only additional step was to install tcsh because when I tried tkmedit it returned: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: File or directory not found.
My machine is an Alienware MX17R2 with 8GB RAM and Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz (Quadcore) My video from lspci is Advanced Micro Devices [AMD] nee ATI Broadway XT [Mobility Radeon HD 5800 Series] and I am using native drivers instead of AMD proprietary driver
thank you for your support
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Marcos Martins da Silva -
Nick Schmansky